Protein ID Gene symbol D/H ratio p-value Number of sample pairs pI /mass (kDa) Number of peptides Swiss prot accession number Sequence coverage (%) Increased release Protein AMBP AMBP 2.0 ~ 14.2 0.016* 6/7 5.95 / 40.46 122 P02760 45 Prostaglandin-H2 D-isomerase PTGDS 1.6 ~ 11.8 0.0239* 6/7 7.66 / 21.56 23 P41222 42 Uromodulin UMOD 2.9 ~ 30.5 0.164 5/7 5.05 / 72.96 90 P07911 44 Beta-2-glycoprotein 1 APOH 2.4 ~ 35.8 0.101 5/7 8.34 / 40.55 2 P02749 14 Plasma serine protease inhibitor SERPINA5 2.3 ~ 17.3 0.0417* 5/7 9.3 / 46.53 19 P05154 28 Lysosomal alpha-glucosidase GAA 2.6 ~ 8.5 0.013* 5/7 5.62 / 106.59 5 P10253 17 Ig kappa chain V-III region SIE KV302 1.6 ~ 18.1 0.216 5/7 8.72 / 11.98 4 P01620 39 Ig lambda-2 chain C IGLC2 2.1 ~ 10.9 0.157 4/7 6.92 / 11.69 17 P0CG05 69 Kininogen-1 KNG1 2.7 ~ 28.4 0.108 4/7 6.34 / 74.43 62 P01042 37 Basement membrane-specific heparan sulfate proteoglycan core protein HSPG2 3.2 ~ 13.2 0.082 4/7 6.06 / 481.43 35 Q2VPA1 10 Polymeric immunoglobulin receptor PIGR 2.0 ~ 17.7 0.165 4/7 5.58 / 85.78 5 P01833 24 Ribonuclease RNASE1 4.5 ~ 30.3 0.099 4/7 9.1 / 18.38 13 P07998 37 Ig kappa chain C region IGKC 1.6 ~ 13.7 0.158 4/7 5.58 / 12.00 62 P01834 80 Pro-epidermal growth factor EGF 1.8 ~ 19.5 0.243 4/7 5.53 / 139.41 2 P01133 12 Reduced release Serotransferrin TF 0.03 ~ 0.14 0.181 6/7 6.81 / 81.15 35 P02787 33 Alpha-1-antitrypsin SERPINA1 0.08 ~ 0.31 <0.0001* 6/7 5.37 / 47.83 49 P01009 36 Ig gamma-2 chain C IGHG2 0.03 ~ 0.47 0.920 5/7 7.66 / 37.18 31 P01859 31 Alpha-1B-glycoprotein A1BG 0.07 ~ 0.35 0.976 5/7 5.56 / 55.10 3 P04217 24 Zinc-alpha-2-glycoprotein AZGP1 0.05 ~ 0.2 0.500 4/7 5.71 / 35.11 9 P25311 39 Zinc-alpha-2-glycoprotein SERPINA3 0.28 ~ 0.5 0.716 4/7 5.33 / 48.52 32 P01011 36 Serum albumin ALB 0.04 ~ 0.41 0.003 4/7 5.92 / 73.00 322 P02768 66 Protein expression ratios of D/H shown here cover the range of seven measurements. D = Deuterium labeling on peptide fragments of proteins from HCC urine; H = Hydrogen labeling on peptide fragments of proteins from control of normal counterpart) *Statistically significant data by student t-test (p<0.05)0

Table 1: Increased (D/H ratio ≥ 1.5) and decreased expression (D/H ratio ≤ 0.6) proteins were displayed in at least four of seven hepatocellular carcinoma (HCC) urine sample pairs when identified by nanoLC-MS/MS coupled with stable isotope dimethyl labeling.